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INSTALL
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INSTALL
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Bio::EnsEMBL::XS
Version 2.3.2
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
OBTAINING THE ENSEMBL API EXTENSIONS
------------------------------------
The latest version can be obtained by cloning the GitHub repo::
git clone https://github.com/Ensembl/ensembl-xs.git
PREREQUISITES
-------------
The Ensembl API extensions require an installation of the Ensembl Perl API.
See http://www.ensembl.org/info/docs/api/api_installation.html for instructions
on how to install the API.
Like the Ensembl API, the extensions are designed to run with all perl versions >= 5.8.9.
QUICK INSTALL
-------------
The Ensembl API extensions can be be installed from source code.
To install the extensions from the command line:
$ cd ensembl-xs # assume ensembl-xs is the directory name of the cloned repo
$ perl Makefile.PL
$ make
$ make test
$ make install # may need root access
After the installation, the user may continue to use the Ensembl API as usual, since
this will now automatically detect the availability of the extensions and use them where
appropriate.
BUILDING AND TESTING
--------------------
This section describes the "make" and "make test" commands which build
and test the Ensembl API extensions. If you ran these without incident,
then you can probably skip this section.
The 'make' command will build the extensions modules in the
usual manner.
make
The 'make test' command runs the test scripts in the 'xs/t' subdirectory.
make test
BENCHMARKING
------------
The 'bin/' directory of the distribution contains a bunch of perl scripts which compare
the running time of the original procedures in the Ensembl API and of the corresponding
extensions.
Each script runs tests for one single procedure, e.g. to benchmark the 'rearrange' method
of module Bio::EnsEMBL::Utils::Argument against its reimplementation:
$ cd bin
$ perl rearrange-bench.pl
Each script runs the original and optimised version on a set of tasks and for each one
it shows a comparison of the running time in the two cases.
INSTALLATION
------------
This section describes the final installation of the Ensembl API extensions
via the "make install".
The 'make install' will install the modules and scripts on your system.
You may need administrator privileges to perform this task.
Alternately you can can install the extensions to a local
directory (see ExtUtils::MakeMaker for full details), e.g.
$ perl Makefile.PL PREFIX=/home/user
Don't forget to update your PERL5LIB environment variable if you do
this, or add a line to your script to tell Perl where to find the files,
e.g.
use lib qw( /home/user/lib/perl5/site_perl/5.10.0 );
AUTHOR
------
The module and the extensions have been written by Alessandro Vullo <[email protected]>
with the assistance of Andy Yates and contribution of Will McLaren.
LICENSE AND COPYRIGHT
---------------------
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.